Illustration of the simulated DNA molecules and the polymerase position. Only a single strand of the molecule is represented by the read sequence. The total number of molecules modeled is N, and this would be a snapshot at a later flow, where the polymerase has progressed and dephasing is visible (demonstrated by pos[0] being at a different base than pos[1]). An array pos[ ] stores the position of the polymerase associated with each of the N molecules, and its values are initialized to the beginning of the read sequence.